class: center, middle, inverse, title-slide .title[ # What does a Global Fish Community Time-series Database Tell us about Biodiversity Trends in Freshwater Environments? ] .subtitle[ ## Joint Aquatic Sciences Meeting 2022 ] .author[ ###
Alain Danet
, Xingli Giam, Julian Olden, Lise Comte ] .author[ ### Illinois State University ] .author[ ###
https://alaindanet.github.io
] .date[ ### Slides created via the R package
xaringan
] --- <div style = "position:fixed; visibility: hidden"> `$$\require{color}\definecolor{red}{rgb}{1, 0, 0}$$` `$$\require{color}\definecolor{green}{rgb}{0, 1, 0}$$` `$$\require{color}\definecolor{blue}{rgb}{0, 0, 1}$$` </div> <script type="text/x-mathjax-config"> MathJax.Hub.Config({ TeX: { Macros: { red: ["{\\color{red}{#1}}", 1], green: ["{\\color{green}{#1}}", 1], blue: ["{\\color{blue}{#1}}", 1] }, loader: {load: ['[tex]/color']}, tex: {packages: {'[+]': ['color']}} } }); </script> <style> .red {color: #FF0000;} .green {color: #00FF00;} .blue {color: #0000FF;} </style> # Biodiversity in crisis <img src="data:image/png;base64,#images/Bending-the-Curve_PR.jpg" width="70%" style="display: block; margin: auto;" /> .footnote[[Newbold, et al. (2015)](https://www.nature.com/articles/nature14324); [IPBES, (2019)](https://ipbes.net/sites/default/files/2020-02/ipbes_global_assessment_report_summary_for_policymakers_fr.pdf), [Image credit: UNEP](https://production-wordpress.unep-wcmc.org/content//uploads/2021/11/Bending-the-Curve_PR.jpg)] ??? Scientists reach a consensus on the fact that biodiversity is going through an unprecedented crisis. Predictions indicates that if we do not act strongly and quickly, this crisis could have dramatic consequences that have not been seen yet. --- # Freshwater fishes <img src="data:image/png;base64,#images/wat21208-toc-0001-m.jpg" width="58%" style="display: block; margin: auto;" /> <!--https://wires.onlinelibrary.wiley.com/cms/asset/b9c85273-0008-4bb3-be85-e390ec0dcaa9/wat21208-toc-0001-m.jpg--> .footnote[[He, et al. (2017)](https://onlinelibrary.wiley.com/doi/abs/10.1002/wat2.1208); [Reid, et al. (2019a)](https://onlinelibrary.wiley.com/doi/abs/10.1111/brv.12480); [IPBES, (2019)](https://ipbes.net/sites/default/files/2020-02/ipbes_global_assessment_report_summary_for_policymakers_fr.pdf)] ??? This is particularly true for freshwater ecosystems. Although freshwater constitute 0.01% of water on earth, they host almost 9.5% of Earth described species. Freshwater biodiversity is threatened by terrestrial land degradation, overexploitation, pollution, flow alteration and species alteration. However we know little on temporal dynamics of freshwater fishes are affected by those anthropogenic pressures. --- # Describing biodiversity changes .footnote[Image: [worldwildlife.org](https://files.worldwildlife.org/wwfcmsprod/images/Buffalo_fish/story_full_width/80b2nhfpi6_Buffalo_fish__c__Freshwaters_Illustrated.jpg)] .pull-left[ <img src="data:image/png;base64,#https://files.worldwildlife.org/wwfcmsprod/images/Buffalo_fish/story_full_width/80b2nhfpi6_Buffalo_fish__c__Freshwaters_Illustrated.jpg" width="100%" style="display: block; margin: auto;" /> ] -- .pull-right[ ## Multidimensional concept 1. Species richness 1. Total abundance 1. Dissimilarity in species composition (P/A or abundance based) ] ??? When an ecologist sampled a community in time, he faces a difficult task. Indeed, how to describe the trends in biodiversity of this community? Is it the number of species, the total abundance, the dissimilarity of the community composition through time? Should I take in account the abundance of the species, in other word, compute Hill numbers ? Of course, this is no one good answer. But measuring several of them, when possible, can help us to refine our understanding biodiversity changes. An alternative hypothesis is that biodiversity trends are similar among them, and that we might need only a few. --- class: center middle # Research questions How do anthropogenic pressures influence the temporal trends of freshwater fish biodiversity? Do different biodiversity facets have the same temporal trends? ??? Regarding the previous research gap, we asked "How do anthropogenic pressures influence the temporal trends of freshwater fish biodiversity?" and "Do different biodiversity facets have the same temporal trends?" --- class: center middle # Methods --- # Fish data: RivFishTime 5359 sites, spanning at least 10 years Homogeneity within sites: protocol, abundance units, sampling period <img src="data:image/png;base64,#images/map_sites.png" width="70%" style="display: block; margin: auto;" /> .footnote[[Comte, et al. (2021)](https://onlinelibrary.wiley.com/doi/abs/10.1111/geb.13210)] ??? To answer those questions, we used the RivFishTime database which contains time series of fish communities spanning at least 10 years. The dataset covers mostly the so called "Western countries": the US and Canada, Western and North Europe, Australia and Japan. For each site, we selected samplings that were identical in terms of protocol, measurement unit and sampling season. After selection, we had more than 5000 sites. --- # Biodiversity facets ## Temporal dissimilarity: - Simpson based dissimilarity - Jaccard (Presence / absence): - Appearance and Disappearance - Turnover and Nestedness ## Species richness and total abundance: - Chao species richness - Total abundance ## Complementary descriptors: exotic species - Percentage of exotic species richness - Percentage of exotic species abundance ??? We characterised biodiversity by temporal dissimilarity of community composition: based on abundance (with Simpson), presence/absence with the Jaccard index. We also decomposed Jaccard in Appearance/Disappearance and Nestedness/Turnover We also described the Coverage based species richness (the Chao) and Total abundance. We also described the composition of communities in terms of exotic species --- # Anthropogenic pressures ## Human footprint (1993; 2009) Based on human infrastructures, land-use, population density <img src="data:image/png;base64,#images/venterfig1.png" width="90%" style="display: block; margin: auto;" /> .footnote[[Venter, et al. (2016b)](https://www.nature.com/articles/ncomms12558)] ??? We described anthropogenic pressures using the Human Footprint index. It is a composite index that take in account human infrastructures, land-use, and various characteristics of human occupation. --- # Hierarchical linear models (INLA) ## General model $$ `\begin{equation} Y_{t} = \alpha + \beta_0Time_t + \sum_{k=1}\beta_{0k}Time_tX_k + \sum_{k=1}\beta_kX_k +\epsilon_{t} \end{equation}` $$ - `\(t\)`: time `\(t\)` --- # Hierarchical linear models (INLA) ## Temporal trends $$ `\begin{equation} Y_{t} = \alpha + \red{\beta_0Time_t} + \sum_{k=1}\beta_{0k}Time_tX_k + \sum_{k=1}\beta_kX_k +\epsilon_{t} \end{equation}` $$ - `\(t\)`: time `\(t\)` --- # Hierarchical linear models (INLA) ## Effect of anthropogenic pressures on temporal trends $$ `\begin{equation} Y_{t} = \alpha + \beta_0Time_t + \red{\sum_{k=1}\beta_{0k}Time_tX_k} + \sum_{k=1}\beta_kX_k +\epsilon_{t} \end{equation}` $$ - `\(t\)`: time `\(t\)` - `\(X_k\)`: Anthropogenic pressure `\(k\)`: - Legacy of past anthropogenic pressure: Human footprint (1993) - Recent changes in anthropogenic pressure: ratio of Human footprint (2009/1993) --- # Hierarchical linear models (INLA) ## Control for main effects of anthropogenic pressure $$ `\begin{equation} Y_{t} = \alpha + \beta_0Time_t + \sum_{k=1}\beta_{0k}Time_tX_k + \red{\sum_{k=1}\beta_kX_k} +\epsilon_{t} \end{equation}` $$ - `\(t\)`: time `\(t\)` - `\(X_k\)`: Anthropogenic pressure `\(k\)`: - Legacy of past anthropogenic pressure: Human footprint (1993) - Recent changes in anthropogenic pressure: ratio of Human footprint (2009/1993) --- # Hierarchical linear models (INLA) ## Random effects to estimate temporal trends at basin (m) and site scale (i|m) $$ `\begin{equation} Y_{t, \red{i|m}} = \blue{\alpha} + \green{\beta_0}Time_t + \sum_{k=1}\beta_{0k}Time_tX_k + \sum_{k=1}\beta_kX_k +\epsilon_{t} \end{equation}` $$ - Intercept: `\(\blue{\alpha = \alpha_0 + a_{i|m} + a_m}\)` - Slope estimating temporal trends: `\(\green{\beta_0 = \mu + b_{i|m} + b_m}\)` - `\(a_{i|m}, a_m, b_{i|m}, b_m \sim \mathcal{N}(0,\,\sigma^{2})\)` ??? We added random effects on the intercept, alpha and on the temporal trends quantified by the slope beta 0. The variance of the intercept and the temporal trends were dependent on the hydrographic basin and on the site, nested within the basin effect. --- # Hierarchical linear models (INLA) $$ `\begin{equation} Y_{t} = \alpha + \red{\beta_0}Time_t + \sum_{k=1}\red{\beta_{0k}}Time_tX_k + \sum_{k=1}\beta_kX_k +\epsilon_{t} \end{equation}` $$ - Time and interactions: - Time - Time x Legacy of long term pressure (Human footprint 1993) - Time x Recent change in pressure (Ratio of Human footprint 2009/1993) ??? Today, I will show you only the effect of time (the temporal trends) and its interaction with the legacy of long term pressure, the Human footprint of the year 1993 and the recent change in pressure quantified by the ratio between the human footprint of 2009 and the one of 1993 --- class: center, middle, large # Results How do anthropogenic pressures influence the temporal trends of freshwater fish biodiversity? ??? Now, How do anthropogenic pressures influence the temporal trends of freshwater fish biodiversity? --- # Temporal dissimilarity <img src="data:image/png;base64,#jasm2022_files/figure-html/unnamed-chunk-11-1.png" width="70%" style="display: block; margin: auto;" /> ??? First the results temporal dissimilarity. At the x axis, I displayed the standardized slope coefficients. At the Y axis, I displayed the effect of time, the temporal trends and how the temporal trends is affected by the Legacy of anthropogenic pressures, the recent changes in pressure and their interaction. --- class: center # Temporal dissimilarity Legacy of past and recent human pressure increase temporal turnover <img src="data:image/png;base64,#jasm2022_files/figure-html/unnamed-chunk-12-1.png" width="70%" style="display: block; margin: auto;" /> ??? Our results showed both the legacy and recent changes in anthropogenic pressures accelerates changes in species composition, and that they have a synergistic effect. --- # Abundance and richness <img src="data:image/png;base64,#jasm2022_files/figure-html/unnamed-chunk-16-1.png" width="70%" style="display: block; margin: auto;" /> ??? Now, the same question with the total abundance, species richness and the percentage of exotic species in the communities. --- class:center # Abundance and richness Positive temporal trends ([Klink, et al., 2020](https://science.sciencemag.org/content/368/6489/417)), modulated by anthropogenic pressures <img src="data:image/png;base64,#jasm2022_files/figure-html/unnamed-chunk-17-1.png" width="70%" style="display: block; margin: auto;" /> ??? We found a global positive temporal trends, confirming previous results. We also see that legacy increase the temporal trends of total abundance and species richness. Recent increase in anthropogenic pressure decrease temporal trends of abundance and richness but increase the one of percentage of exotic species. --- class:center # Abundance and richness Positive temporal trends ([Klink, et al., 2020](https://science.sciencemag.org/content/368/6489/417)), modulated by anthropogenic pressures <img src="data:image/png;base64,#jasm2022_files/figure-html/unnamed-chunk-18-1.png" width="70%" style="display: block; margin: auto;" /> ??? We found a global positive temporal trends, confirming previous results. We also see that legacy increase the temporal trends of total abundance and species richness. Recent increase in anthropogenic pressure decrease temporal trends of abundance and richness but increase the one of percentage of exotic species. --- class:center # Abundance and richness Positive temporal trends ([Klink, et al., 2020](https://science.sciencemag.org/content/368/6489/417)), modulated by anthropogenic pressures <img src="data:image/png;base64,#jasm2022_files/figure-html/unnamed-chunk-19-1.png" width="70%" style="display: block; margin: auto;" /> ??? We found a global positive temporal trends, confirming previous results. We also see that legacy increase the temporal trends of total abundance and species richness. Recent increase in anthropogenic pressure decrease temporal trends of abundance and richness but increase the one of percentage of exotic species. --- class: center, middle, large # Typology of biodiversity temporal trends Do different biodiversity facets have the same temporal trends? ??? Now, Do different biodiversity facets have the same temporal trends? --- class: center # Typology of biodiversity temporal trends Three dimensions: Dissimilarity, Species richness ([Dornelas, et al., 2014](https://science.sciencemag.org/content/344/6181/296)), Total abundance <img src="data:image/png;base64,#jasm2022_files/figure-html/unnamed-chunk-21-1.png" width="80%" style="display: block; margin: auto;" /> ??? The PCA over the temporal trends displayed a first axis related to dissimilarity measurement, a second related to species richness and the fourth axis to Total abundance temporal trends --- class: center, middle # Take home messages **Past and recent anthropogenic pressures** interacts to drive biodiversity trends in fish freshwater communities **Several dimensions** of temporal trends of biodiversity ??? So far, I showed you that **Past and recent anthropogenic pressures** affect and interact to drive biodiversity trends in fish freshwater communities **Several dimensions** of temporal trends of biodiversity So it might be necessary to assess them simultaneously --- # Thanks <img src="data:image/png;base64,#images/collab_isu.png" width="70%" style="display: block; margin: auto;" /> ??? I want to warmly thank my post doc supervisors for the great collaboration, Lise, Xingli and Julian --- class: center, middle # Thanks We are indebt to all the researchers and agencies who monitored fish abundance through time and provided their data for this project. Lise Comte achieved the Herculean task to assemble RivFishTime ([Comte, et al., 2021](https://onlinelibrary.wiley.com/doi/abs/10.1111/geb.13210)). Thank you for listening to me! Any questions? https://alaindanet.github.io **Past and recent anthropogenic pressures** interacts to drive biodiversity trends in fish freshwater communities **Several dimensions** of temporal trends of biodiversity ??? I would like to put forward the tremendous work of all the researchers and agencies over the world who monitored fish abundance through time and provided their data for this project. I would also like to highlight the herculean work of Lise Comte in assembling the RivFishTime database! Thank you!